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- PDB-2h77: Crystal structure of human TR alpha bound T3 in monoclinic space group -

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Basic information

Entry
Database: PDB / ID: 2h77
TitleCrystal structure of human TR alpha bound T3 in monoclinic space group
ComponentsTHRA protein
KeywordsHORMONE/GROWTH FACTOR / TR alpha / T3 / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


regulation of myeloid cell apoptotic process / negative regulation of DNA-templated transcription initiation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / female courtship behavior / regulation of lipid catabolic process / thyroid hormone receptor signaling pathway / positive regulation of thyroid hormone receptor signaling pathway / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / cartilage condensation ...regulation of myeloid cell apoptotic process / negative regulation of DNA-templated transcription initiation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / female courtship behavior / regulation of lipid catabolic process / thyroid hormone receptor signaling pathway / positive regulation of thyroid hormone receptor signaling pathway / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / cartilage condensation / regulation of heart contraction / type I pneumocyte differentiation / thyroid hormone binding / thyroid gland development / general transcription initiation factor binding / retinoic acid receptor signaling pathway / TBP-class protein binding / hormone-mediated signaling pathway / response to cold / ossification / erythrocyte differentiation / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / chromatin DNA binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / positive regulation of cold-induced thermogenesis / transcription by RNA polymerase II / cell differentiation / learning or memory / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Thyroid hormone receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Thyroid hormone receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
3,5,3'TRIIODOTHYRONINE / Thyroid hormone receptor alpha / Thyroid hormone receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsNascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R. / Bleicher, L. / Ambrosio, A.L.B. / Figueira, A.C.M. / Santos, M.A.M. / Neto, M.O. / Fischer, H. ...Nascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R. / Bleicher, L. / Ambrosio, A.L.B. / Figueira, A.C.M. / Santos, M.A.M. / Neto, M.O. / Fischer, H. / Togashi, H.F.M. / Craievich, A.F. / Garrat, R.C. / Baxter, J.D. / Webb, P. / Polikarpov, I.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural rearrangements in the thyroid hormone receptor hinge domain and their putative role in the receptor function.
Authors: Nascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R. / Ambrosio, A.L.B. / Bleicher, L. / Figueira, A.C.M. / Santos, M.A.M. / Neto, M.O. / Fischer, H. / Togashi, M. / Craievich, A.F. ...Authors: Nascimento, A.S. / Dias, S.M.G. / Nunes, F.M. / Aparicio, R. / Ambrosio, A.L.B. / Bleicher, L. / Figueira, A.C.M. / Santos, M.A.M. / Neto, M.O. / Fischer, H. / Togashi, M. / Craievich, A.F. / Garratt, R.C. / Baxter, J.D. / Webb, P. / Polikarpov, I.
History
DepositionJun 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Structure summary / Category: audit_author / software
Item: _audit_author.name / _software.classification ..._audit_author.name / _software.classification / _software.name / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THRA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6292
Polymers30,9781
Non-polymers6511
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.569, 80.626, 62.614
Angle α, β, γ (deg.)90.000, 121.090, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein THRA protein


Mass: 30978.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THRA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q6FH41, UniProt: P10827*PLUS
#2: Chemical ChemComp-T3 / 3,5,3'TRIIODOTHYRONINE / T3 / THYROID HORMONE / LIOTHYRONINE


Mass: 650.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12I3NO4 / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.33 Å3/Da / Density % sol: 71.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.0 M sodium cacodylate and 0.1M sodium acetate threehydrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2004 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.33→62.994 Å / Num. all: 18468 / Num. obs: 18468 / % possible obs: 86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.33-2.461.70.3832476728070.38390
2.46-2.611.70.2872.7454426500.28789.6
2.61-2.781.80.2093.7431724620.20988.7
2.78-3.011.80.164.7406023010.1688.3
3.01-3.31.80.1057.2372220610.10586.6
3.3-3.681.90.06112.2336018160.06184.3
3.68-4.251.90.05114.1302815950.05183.4
4.25-5.2120.05312.9254612940.05380.6
5.21-7.3720.06211.119779740.06277.5
7.37-35.542.10.04810.110685080.04871.9

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Phasing

Phasing MRRfactor: 0.313 / Cor.coef. Fo:Fc: 0.753
Highest resolutionLowest resolution
Rotation3 Å35.54 Å
Translation3 Å35.54 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345data collection
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→32.22 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.588 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.207
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 942 5.1 %RANDOM
Rwork0.187 ---
all0.19 18468 --
obs0.19 18467 85.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.043 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.03 Å2
2--0 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.33→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 23 70 2140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222117
X-RAY DIFFRACTIONr_angle_refined_deg2.6171.9982866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5285256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01623.97893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.90415376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9241514
X-RAY DIFFRACTIONr_chiral_restr0.1540.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021579
X-RAY DIFFRACTIONr_nbd_refined0.2240.2940
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21390
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2460.273
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3720.25
X-RAY DIFFRACTIONr_mcbond_it1.2641.51307
X-RAY DIFFRACTIONr_mcangle_it2.06622079
X-RAY DIFFRACTIONr_scbond_it3.3473894
X-RAY DIFFRACTIONr_scangle_it4.9344.5786
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 66 -
Rwork0.258 1362 -
obs-1428 90.27 %

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